Blender not responding while running my script
Short answer: No
See: Strange errors using ‘threading’ module

Python scripts run 'blocking', Blender will wait until finsihed. It isn't thread-safe to run python in parallel. You may be able to get around the issues with Blender crashing with python running own threads using a modal operator with timer: Blender UI Multithreading Progressbar. Also consider if a modal operator running the background is suitable for your use case (let it return {'PASS_THROUGH'}).

If your scripts run for hours, you should also investigate why they are so slow. See here what hurts performance: Python performance with Blender operators